Is the fish eating normally? (What are you feeding it?) Do you notice aggression? (You really need to observe this closely, as aggression is not always so obvious. Does the fish cower in a corner, is timid to eat, breathing rapidly, has any torn fins?)
Do the brown spots actually look like a brown skin color rather then an actual growth or spot on the fish? As if the spot is a fading of the color to brownish? Do you notice this all the time, or just during some times?